+
+
+
Scores and documentation of ACMG evidence criteria used for variant classification
+in CPSR
+
+
+
A list object with three elements: 'score2tier', 'evidence_codes',
+'pathogenic_range_gnomad'
+
score2tier - A data frame with 5 rows and two columns that indicate
+current score thresholds for variant classification in CPSR:
CPSR_CLASSIFICATION - variant classification level (P, LP, VUS etc)
CPSR_PATHOGENICITY_SCORE - indication of CPSR "score bucket" for a given
+classification (HTML string)
#' @format evidence_codes - A data frame with 34 rows and 7 columns that document
+all ACMG evidence criteria that are used for variant classification in CPSR:
cpsr_evidence_code - code for evidence criterion ('ACMG_BA1_AD' etc)
category - type of evidence feature ('clinpop','funcvarpop','funcvar','funccomp')
pathogenicity_pole - whether the given evidence support a benign variant character ('B'), or
+pathogenic character ('P')
category_long - long version of 'category' column
description - Verbose description for the given evidence criterion
sherloc_code - Corresponding code identifier in SherLoc (Nykamp et al., GiM, 2017)
path_score - Score associated with the given evidence criterion (negative or positive)